Implementation of an XML-based user interface with applications in ice sheet modeling

The scientific domain presents unique challenges to software developers. This thesis describes the application of design patterns to the problem of dynamically changing interfaces to scientific application software (GLIMMER, which performs ice sheet modeling). In its present form, GLIMMER uses a text configuration file to define model behavior, set parameters, and structure model input/output (I/O). The creation of the configuration file presents a significant problem to users due to its format and complexity. GLIMMER is still under development, and the number of changes to configuration parameters, parameter types, and parameter dependencies makes devel-opment of any single interface of use only for a short term. The application of design patterns described here resulted in an interface specification tool that then generates multiple versions of a user interface usable across a wide variety of configuration pa-rameter types, values, and dependencies. The resulting products have leveraged de-sign patterns and solved problems associated with design pattern usage not found in the specialized software engineering literature

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

A Pattern Language for High-Performance Computing Resilience

High-performance computing systems (HPC) provide powerful capabilities for modeling, simulation, and data analytics for a broad class of computational problems. They enable extreme performance of the order of quadrillion floating-point arithmetic calculations per second by aggregating the power of millions of compute, memory, networking and storage components. With the rapidly growing scale and complexity of HPC systems for achieving even greater performance, ensuring their reliable operation in the face of system degradations and failures is a critical challenge. System fault events often lead the scientific applications to produce incorrect results, or may even cause their untimely termination. The sheer number of components in modern extreme-scale HPC systems and the complex interactions and dependencies among the hardware and software components, the applications, and the physical environment makes the design of practical solutions that support fault resilience a complex undertaking. To manage this complexity, we developed a methodology for designing HPC resilience solutions using design patterns. We codified the well-known techniques for handling faults, errors and failures that have been devised, applied and improved upon over the past three decades in the form of design patterns. In this paper, we present a pattern language to enable a structured approach to the development of HPC resilience solutions. The pattern language reveals the relations among the resilience patterns and provides the means to explore alternative techniques for handling a specific fault model that may have different efficiency and complexity characteristics. Using the pattern language enables the design and implementation of comprehensive resilience solutions as a set of interconnected resilience patterns that can be instantiated across layers of the system stack.Comment: Proceedings of the 22nd European Conference on Pattern Languages of Program

Finite difference methods fengshui: alignment through a mathematics of arrays

Numerous scientific-computational domains make use of array data. The core computing of the numerical methods and the algorithms involved is related to multi-dimensional array manipulation. Memory layout and the access patterns of that data are crucial to the optimal performance of the array-based computations. As we move towards exascale computing, writing portable code for efficient data parallel computations is increasingly requiring an abstract productive working environment. To that end, we present the design of a framework for optimizing scientific array-based computations, building a case study for a Partial Differential Equations solver. By embedding the Mathematics of Arrays formalism in the Magnolia programming language, we assemble a software stack capable of abstracting the continuous high-level application layer from the discrete formulation of the collective array-based numerical methods and algorithms and the final detailed low-level code. The case study lays the groundwork for achieving optimized memory layout and efficient computations while preserving a stable abstraction layer independent of underlying algorithms and changes in the architecture.Peer ReviewedPostprint (author's final draft

Identificación de patrones de diseño para software científico a partir de esquemas preconceptuales

Los patrones de diseño son soluciones a problemas de diseño recurrentes en software científico. Estos patrones se usan para mitigar la ausencia de algunos aspectos de calidad inherentes al software. Los científicos, debido a su formación profesional, abordan diseños poco flexibles y difíciles de mantener en sus aplicaciones. Además, en ausencia de un lenguaje común con ingenieros de software se hace muy compleja la comunicación y validación del dominio de aplicación. Normalmente, las representaciones de los patrones de diseño se basan en diagramas de UML u otro tipo de grafos. Estos diagramas son difíciles de entender para los científicos e ingenieros de software inexpertos debido a su nivel de formalismo y, además, porque sólo representan el patrón de diseño aplicado y no el problema genérico que resuelven. Por otro lado, estos diagramas como unidad no poseen los elementos necesarios para representar completamente un dominio de software científico y se deben valer de la combinación de varios de ellos para hacerlo. Por ello, en esta Tesis de Maestría se propone una representación en esquemas preconceptuales de los patrones de diseño más usados en software científico y, además, la representación genérica del problema que resuelven. Adicionalmente, se presentan una serie de nuevos elementos para los esquemas preconceptuales que permiten la completa representación y validación de los dominios complejos presentes en el software científico. Al usar esquemas preconceptuales se facilita el entendimiento de los patrones de diseño debido a su proximidad con el lenguaje natural y a los elementos disponibles para su representación. Además, se hace posible la comunicación y validación del dominio de aplicación entre científicos e ingenieros de software. Este trabajo ayuda a la comunidad científica a hacer un diseño más robusto, flexible y fácil de mantener de su aplicación, y además, abre las puertas a la automatización de la implementación de los patrones de diseño a partir de una representación del dominio en esquemas preconceptuales.Abstract: Design patterns are solutions for recurrent design problems in scientific software. These patterns are used to mitigate the lack of several quality aspects inherent in the software. Scientists, due to their professional training, tackle little flexible and maintainable designs for their software applications. In addition, in the absence of a common vocabulary with software engineers, domain communication and validation becomes complex. Normally, design patterns representation are based on UML class diagrams or other kind of graphs. These diagrams are difficult to understand for scientist and inexperienced software engineers due to their level of formalism and, also because of this diagrams only represents the implemented design pattern and not the generic problem the design patterns solves. Furthermore, these diagrams as unity do not have the necessary elements to represent scientific software domains completely, so they must combine to do it. For this reason, in this Master’s Thesis it is proposed a representation of design patterns for scientific software by using preconceptual schemes, and also, a generic representation of the problem that design patterns address. Additionally, it is proposed a number of new elements for preconceptual schemes that allows a complete representation and validation of complex domains in scientific software. By using preconceptual schemes facilitates design patterns understanding due to their natural language proximity. In addition, it is made possible the validation and communication of application domain between scientists and software engineers. This work helps scientific community to make robust, flexible and maintainable software applications, and also, opens the doors to automated design pattern implementation from domain representation in preconceptual schemes.Maestrí

Reusable Solutions for Implementing Usability Functionalities

Electronic version of an article published as International Journal of Software Engineering and Knowledge Engineering, Volume 25, Issue 04, May 2015, 727 http://dx.doi.org/10.1142/S0218194015500084 © World Scientific Publishing Company http://www.worldscientific.com/worldscinet/ijsekeUsability is a software system quality attribute. Although software engineers originally considered usability to be related exclusively to the user interface, it was later found to affect the core functionality of software applications. As of then, proposals for addressing usability at different stages of the software development cycle were researched. The objective of this paper is to present three reusable solutions at detailed design and programming level in order to effectively implement the Abort Operation, Progress Feedback and Preferences usability functionalities in web applications. To do this, an inductive research method was applied. We developed three web applications including the above usability functionalities as case studies. We looked for commonalities across the implementations in order to induce a general solution. The elements common to all three developed applications include: application scenarios, functionalities, responsibilities, classes, methods, attributes and code snippets. The findings were specified as an implementation-oriented design pattern and as programming patterns in three languages. Additional case studies were conducted in order to validate the proposed solution. The independent developers used the patterns to implement different applications for each case study. As a result, we found that solutions specified as patterns can be reused to develop web applications.This work has been funded by the Spanish Ministry of Science and Innovation “Tecnologías para la Replicación y Síntesis de Experimentos en IS” (TIN2011-23216) and “Go Lite” (TIN2011-24139) projects

Averting Denver Airports on a Chip

As a result of recent advances in software engineering capabilities, we are now in a more stable environment. De-facto hardware and software standards are emerging. Work on software architecture and design patterns signals a consensus on the importance of early system-level design decisions, and agreements on the uses of certain paradigmatic software structures. We now routinely build systems that would have been risky or infeasible a few years ago. Unfortunately, technological developments threaten to destabilize software design again. Systems designed around novel computing and peripheral devices will spark ambitious new projects that will stress current software design and engineering capabilities. Micro-electro-mechanical systems (MEMS) and related technologies provide the physical basis for new systems with the potential to produce this kind of destabilizing effect. One important response to anticipated software engineering and design difficulties is carefully directed engineering-scientific research. Two specific problems meriting substantial research attention are: A lack of sufficient means to build software systems by generating, extending, specializing, and integrating large-scale reusable components; and a lack of adequate computational and analytic tools to extend and aid engineers in maintaining intellectual control over complex software designs

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies